Summary stats

General stats about the patient cohort

Stat Value
Unique HPO terms 24
Cohort size 1932
Rejected patients by empty profile 0
HPOs per patient (average) 4.0399
HPO terms per patient: percentile 90 3
Percentage of HPO with more specific children 78.6547
DsI for uniq HP terms 0
DsI for frequency weigthed HP terms 0
Number of unknown phenotypes 0
Number of clusters with mutations accross > 1 chromosomes 1078
Average variant size 3498347.164
Nucleotides affected by mutations 1266576677
Number of genome windows 860
Mean patients per genome window 2.4942
Number of genome window shared by >= 2 patients 466
Number of patients with at least 1 SOR 562
Nucleotides affected by mutations 522948664

HPO stats

HPOs more frequent in the cohort

HPO Patient percentage
Cognitive impairment 93.42650103519668
Intellectual disability, mild 29.244306418219463
Intellectual disability, severe 28.93374741200828
Short stature 27.173913043478258
Seizure 26.501035196687372
Autistic behavior 25.77639751552795
Hypotonia 25.62111801242236
Microcephaly 21.790890269151138
Behavioral abnormality 19.875776397515526
Intellectual disability, moderate 18.944099378881987
Intrauterine growth retardation 15.217391304347828
Morphological central nervous system abnormality 13.043478260869565
Abnormal external genitalia 11.438923395445135
Attention deficit hyperactivity disorder 9.109730848861282
Macrocephaly 7.815734989648034
Abnormal cardiac septum morphology 6.625258799171843
Abnormality of the upper urinary tract 5.331262939958592
Conotruncal defect 4.917184265010352
Tall stature 4.3478260869565215
Abnormal heart valve morphology 3.002070393374741
Abnormality of the lower urinary tract 2.898550724637681
Abnormality of cardiovascular system morphology 1.8633540372670807
Abnormal internal genitalia 0.6211180124223602
Abnormality of the genitourinary system 0.4658385093167702

Cohort genome coverage analysis

Distribution of the genome coverage of all mutations characterized in the cohort. Second figure shows the same results for SORs.

Distribution of mutations

Distribution of all mutations along the genome (Length) and the number of patients that have at least one of them (Count). Second figure shows the same for SORs.

HPO annotations distribution

Analysis of the HPO terms within the HPO ontology and the cohort of patients. Left: distribution of terms within the ontology and the cohort. Right: percentage of terms distribution within the ontology and the cohort.

HPOs frequency distribution. Colour based on the HPO frequency.

Clustering patients by HPO profile

All patients are clustered using their HPO profiles. First figure shows the information coefficient distribution for the top clusters. Second figure shows which chromosomes are affected in the patients for each top cluster.

HPO profile redundancy

For each patient profile size (number of phenotypes, x-axis) it is shown the number of HPO phenotypes that are parent of other terms within the profile (number of parent terms, y-axis).

HPO ICs distribution

First figure shows the ICs distribution in terms of the HP ontology (x-axis) and for each single HPO term, its frequency in the cohort according to the HP ontology structure (y-axis) and the second figure shows the same distributions considering the profiles analyzed.

HPO frequency by cluster

Patients in Cluster 0 Phenotypes Frequency
66 Cognitive impairment, Intellectual disability, mild, Autistic behavior 100.0, 100.0, 100.0
Patients in Cluster 1 Phenotypes Frequency
63 Cognitive impairment, Intellectual disability, mild, Behavioral abnormality, Abnormal cardiac septum morphology, Abnormality of the genitourinary system 100.0, 100.0, 100.0, 1.5873, 1.5873
Patients in Cluster 2 Phenotypes Frequency
41 Cognitive impairment, Intellectual disability, moderate, Autistic behavior 100.0, 100.0, 100.0
Patients in Cluster 3 Phenotypes Frequency
39 Cognitive impairment, Intellectual disability, severe, Autistic behavior 100.0, 100.0, 100.0
Patients in Cluster 4 Phenotypes Frequency
30 Cognitive impairment, Intellectual disability, mild, Short stature 100.0, 100.0, 100.0
Patients in Cluster 5 Phenotypes Frequency
26 Cognitive impairment, Intellectual disability, severe, Seizure, Abnormal internal genitalia, Abnormal cardiac septum morphology 100.0, 100.0, 100.0, 3.8462, 3.8462
Patients in Cluster 6 Phenotypes Frequency
25 Cognitive impairment, Intellectual disability, severe, Behavioral abnormality, Abnormal internal genitalia 100.0, 100.0, 100.0, 4.0
Patients in Cluster 7 Phenotypes Frequency
22 Cognitive impairment, Intellectual disability, moderate, Hypotonia, Abnormality of the lower urinary tract 100.0, 100.0, 100.0, 4.5455
Patients in Cluster 8 Phenotypes Frequency
21 Cognitive impairment, Intellectual disability, mild, Hypotonia 100.0, 100.0, 100.0
Patients in Cluster 9 Phenotypes Frequency
18 Cognitive impairment, Intellectual disability, severe, Autistic behavior, Seizure 100.0, 100.0, 100.0, 100.0
Patients in Cluster 10 Phenotypes Frequency
18 Cognitive impairment, Intellectual disability, mild, Attention deficit hyperactivity disorder 100.0, 100.0, 100.0
Patients in Cluster 11 Phenotypes Frequency
18 Cognitive impairment, Intellectual disability, moderate, Behavioral abnormality 100.0, 100.0, 100.0
Patients in Cluster 12 Phenotypes Frequency
17 Cognitive impairment, Microcephaly, Short stature 100.0, 100.0, 100.0
Patients in Cluster 13 Phenotypes Frequency
16 Cognitive impairment, Intellectual disability, mild, Macrocephaly, Abnormality of the genitourinary system 100.0, 100.0, 100.0, 6.25
Patients in Cluster 14 Phenotypes Frequency
15 Cognitive impairment, Intellectual disability, severe, Behavioral abnormality, Seizure 100.0, 100.0, 100.0, 100.0
Patients in Cluster 15 Phenotypes Frequency
15 Cognitive impairment, Intellectual disability, severe, Seizure, Hypotonia 100.0, 100.0, 100.0, 100.0
Patients in Cluster 16 Phenotypes Frequency
15 Cognitive impairment, Intellectual disability, mild, Intrauterine growth retardation 100.0, 100.0, 100.0
Patients in Cluster 17 Phenotypes Frequency
14 Cognitive impairment, Intellectual disability, moderate, Autistic behavior, Seizure, Abnormality of the genitourinary system, Abnormal heart valve morphology 100.0, 100.0, 100.0, 100.0, 7.1429, 7.1429
Patients in Cluster 18 Phenotypes Frequency
14 Cognitive impairment, Intellectual disability, moderate, Seizure 100.0, 100.0, 100.0
Patients in Cluster 19 Phenotypes Frequency
14 Cognitive impairment, Intellectual disability, severe, Short stature, Abnormal cardiac septum morphology 100.0, 100.0, 100.0, 7.1429
Patients in Cluster 20 Phenotypes Frequency
13 Cognitive impairment, Intellectual disability, mild, Seizure 100.0, 100.0, 100.0
Patients in Cluster 21 Phenotypes Frequency
13 Cognitive impairment, Intellectual disability, severe, Seizure, Microcephaly 100.0, 100.0, 100.0, 100.0
Patients in Cluster 22 Phenotypes Frequency
11 Cognitive impairment, Seizure, Morphological central nervous system abnormality 100.0, 100.0, 100.0
Patients in Cluster 23 Phenotypes Frequency
11 Cognitive impairment, Autistic behavior, Attention deficit hyperactivity disorder 100.0, 100.0, 100.0
Patients in Cluster 24 Phenotypes Frequency
10 Cognitive impairment, Autistic behavior, Seizure 100.0, 100.0, 100.0

Patient profiles heatmaps

For each patient, their HPO profile similarity coefficient is calculated according to the different methods specified in the analysis and represented in these heatmaps.